Variant rs3895234 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004171.4(SLC1A2):c.562-36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,557,256 control chromosomes in the GnomAD database, including 47,150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3993 hom., cov: 31)

Exomes 𝑓: 0.24 ( 43157 hom. )

Consequence

SLC1A2
NM_004171.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.03

Variant links:

Genes affected

SLC1A2 (HGNC:10940): (solute carrier family 1 member 2) This gene encodes a member of a family of solute transporter proteins. The membrane-bound protein is the principal transporter that clears the excitatory neurotransmitter glutamate from the extracellular space at synapses in the central nervous system. Glutamate clearance is necessary for proper synaptic activation and to prevent neuronal damage from excessive activation of glutamate receptors. Improper regulation of this gene is thought to be associated with several neurological disorders. Alternatively spliced transcript variants of this gene have been identified. [provided by RefSeq, Jun 2017]

SLC1A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 11-35306278-A-G is Benign according to our data. Variant chr11-35306278-A-G is described in ClinVar as [Benign]. Clinvar id is 1332976.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A2	NM_004171.4 linkuse as main transcript	c.562-36T>C		intron_variant		ENST00000278379.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A2	ENST00000278379.9 linkuse as main transcript	c.562-36T>C		intron_variant		1	NM_004171.4	P4	P43004-1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33222

AN:

151680

Hom.:

3976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.0920

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.237

AC:

56272

AN:

237210

Hom.:

7151

AF XY:

0.230

AC XY:

29622

AN XY:

128534

show subpopulations

Gnomad AFR exome

AF:

0.139

Gnomad AMR exome

AF:

0.307

Gnomad ASJ exome

AF:

0.215

Gnomad EAS exome

AF:

0.213

Gnomad SAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.327

Gnomad NFE exome

AF:

0.254

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.243

AC:

341855

AN:

1405460

Hom.:

43157

Cov.:

AF XY:

0.239

AC XY:

166602

AN XY:

697576

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.213

Gnomad4 EAS exome

AF:

0.274

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.318

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.219

AC:

33268

AN:

151796

Hom.:

3993

Cov.:

AF XY:

0.221

AC XY:

16368

AN XY:

74166

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.0912

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.228

Hom.:

748

Bravo

AF:

0.216

Asia WGS

AF:

0.187

AC:

648

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Developmental and epileptic encephalopathy, 41

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.098

DANN

Benign

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over